It was always Rory
by geradsredskittle666
Summary: The Doctor muses on his companions. He was always in love with Rory, not Amy. Warnings: Bisexual Doctor, male/male sexual references. Pairings: Amy/Rory, One sided 11/Rory, mentions of Rose/10, Martha/10, Doctor/Master.


**It was always Rory**

 **Disclaimer: I don't own Dr Who. I don't and never will make money off this work. I use the stories and such for entertainment purposes.**

 **Warnings: Bisexual Doctor, very mild male/male sexual references**

 **Pairings: Amy/Rory, One sided 11/Rory, mentions of Rose/10, Martha/10, Doctor/Master.**

 **AN: To my loyal readers of my other works: I am still working on my current Dr Who stuff and even have most of the next Mea Culpa chapter almost done. I assure you it will be up, but the plot bunnies keep attacking and I am in the middle of at least 5 works (some on paper that need to be typed plus the ones in my head). So I'll get there sometime.**

The Doctor smiled to himself as he watched his two companions. They were his friends. He admitted that now. Even if being friends with him was dangerous. Even if he could never see what they saw in him. He was just a vain old man with a time travelling box that had already gone through a steady stream of human companions to ease his loneliness.

They were his family. They alone had become more than what they were supposed to. He never let his humans too close to him, that only resulted in more pain when they left...or he got them killed...or even worse. He remembered Martha in the year that never was. He remembered Rose that was trapped with his meta crisis version of his tenth regeneration.

Still somehow between the male nurse and his Amelia, they managed to get to his hearts and stubbornly refused to leave. He had soon realised that it was inevitable. So he allowed them in just enough to keep them happy. Of course his darker secrets were kept to himself. He had found that this arrangement of acceptable mutual concern had helped him too. He had helped Amy heal from her husbands 'deaths' or near deaths anyway...or what was reminiscent of deaths by human standards (including every other death style event). He had been able to help her husband deal when his wife was taken. So maybe this family was an inevitable bond for all of them. Made only more sure when their future child and himself were married. This made them a family in law not just bond.

But he knew something deeper was always connecting him and his companions. Love.

Martha had fallen for him.

Rose had fallen even harder than any other for him. Worse still, he had fall in love with her. That childish admiration had given way to something more. He had tried to pretend that he wasn't in love with her. That he didn't notice. But he knew it was plain to see – Mikey had and was upset (and Rose's mother even more so!). Much in the same way Rory had been when The Doctor had stolen _his_ girlfriend as well. Of course The Doctor had not seen it that way, human always confused him like that. He remembered the stern conversation the human had tried to have about it.

 _Remembering_

 _The Doctor had been doing maintenance on the Tardis after his Ponds had gone to bed. He heard steady foot steps but dismissed them as important. Probably just Rory getting some water or tea or whatever humans did to help them get back to sleep. So when he had emerged from under the Tardis The Doctor had been surprised to see Rory. Especially looking so angry at him._

" _So uh whats up Rory?" The Doctor had asked genuinely confused._

 _Rory's eyes narrowed into a glare. "Don't play dumb with me. You know why I'm here..."he had stated._

 _Though The Doctor was just more confused. Had he done anything to harm Amy lately? Nope...he didn't think so. Against his instincts he expressed his confusion. Well he had to admit he wasn't surprised when Rory had pinned him to the Tardis wall in anger. What had he expected honestly? "Err...whatever I did I'm sorry" he said trying to sound solid but it came out as a question._

 _Rory seemed to pause before freeing the timelord. Maybe he was being harsh on the alien he thought to himself. After all he knew The Doctor was stronger than a human, despite what his skinny frame implied. So why would he let Rory harm him? Before he realised it he had releases the alien who just looked like a scared deer in headlights facing a danger that the deer could not understand. That years of evolution had not prepared them for._

 _Rory tried to calm his anger. "So you don't love Amy?" he asked._

 _The Doctor almost laughed but he valued his life. "Amelia? Not in the sense your thinking. She more like a younger sister than what you have with her."_

 _Rory instantly felt bad. He had just reacted in anger and not asked. He had assumed his friend who despite his human appearance was very alien, could understand his human feelings of jealously and felt human feelings of love toward his wife. He had to remind himself that as an ALIEN, his friend had been raised on an ALIEN planet. NOT EARTH._

 _Even worse he had been willing to harm his friend (and more disturbingly his friend had not even tried to fight back). Was such petty feelings worth that? Of course not._

 _Properly ashamed Rory looked away "I should be sorry. I thought you loved her. Wanted her. I thought that stealing her away the night before the wedding was proof. She seems to look at you with more love than me. I guess I should have asked you not assumed or hurt you."_

 _The Doctor looked stunned. He didn't know what to say or how to react._

" _Listen Rory, I felt love once for a human. Long before you and Amy. I could never feel that way about another human female again. She was what Amy is to you. Your wife wasn't ready to marry yet, so she ran away with me. It wasn't the most mature of moves on either her or my parts but whats done is done. When she was ready, she did marry you. Not me, you. She looks at you with affection and love. She looks at me with wonder and excitement. You didn't hurt me. Just a bruise. Timelords are tough." The Doctor explained._

 _The more Rory thought about it, the more he found it true._

 _She had married him._

 _She did love him. Maybe she did love The Doctor also, but it wasn't in the same way._

" _Wait a moment. You said human female. What about human males?" Rory asked suddenly. Then blushed as his thoughts caught up to him. "Not that you have to answer. I mean I shouldn't even ask about that. Do alien even do gay?" he said in a rush._

 _The Doctor laughed. "You humans are so delicate sometimes. Your right I didn't say human males. Guess I haven't fallen deep enough in love yet with one. I mean I have had offers from some attractive men."_

 _Rory looked relieved. "Do you have feelings for anyone?"_

 _The Doctor looked hesitant "yes but he is happy with another. Childhood friends and all that so who am I to say anything?"_

 _END_

The human hadn't asked after that. Still Rory was used to not understanding things when it came to the alien. So why would he?

The Doctor wasn't sure when he had started to love Rory. Maybe it was the adorable way Rory blindly followed like a puppy. Maybe it was the humans confused expressions. Maybe it was the way he panicked when they were in danger.

Or maybe it was the caring nature Rory had. Even if it was an alien that looked as far from human as possible, he still took up his nurse role with ease. Even if he didn't speak the language.

Still to peruse the human would be selfish.

It wasn't that he didn't know how. After all on his home planet he had quite a few male partners. Same-sex partners were not as frowned on as with humans. Well to a point – an unmarried timelord could have as much sex with any gender they wanted. When you got married you had to produce an heir but after that if it was okay with your wife or husband, you could have any amount of partners of any gender again.

He had been with many of the boys in his dorm in the academy. Many did. It was exploration that could only be done before marriage so it was encouraged. One stood out from the haze of moans and groans of his previous partners. The Master. Oh the rival timelord had been quite the charmer. It was love, not lust.

The two had planned to marry after producing successful heirs to their wives. It was an allowable time and no one could deny how they matched each other. Once the heirs were old enough to be an adult, the male roles were no longer needed and even wives left to peruse sexual interests.

The Doctor often wondered why he wanted Rory. It was no secret how opposite the Master and Rory were. Even before the drums in his head sent him insane. The Master and The Doctor had a wild passion that he had yet to feel with another. It was fire and ice and it electrified them both in a way that spurred both men to intense highs. From sexual highs to intense emotional fights that ended in tears or blood. No other way. But both men liked that. The Doctor even suspected that The Master had a kink for pain – both receiving and giving. The tears and blood were ended when they gave in to lust. Make up sex solved all their problems.

With Rory, the feeling was more protective. The nurse was so caring, even to someone as undeserving as The Doctor. More than that, he was so human. A shining example of human too. What could he ever do to deserve that?

No even though every contact with Rory's skin was like electricity and the puppy like innocence made him fall further for the human nurse, Rory was taken. Still The Doctor could protect him. That was enough.

 **A/N: Read and review as always.**


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